I currently have a site that has modifications to Zencart outside of the normal template files. The site is currently down so I can't point you to the site. Zencart itself is very simple set-up. It has a few modules installed, ie. Eway (payment processing), Auspost.
Remote access to the development server can be in the following methods: http (obviously), ftp, ssh. The server OS is Solaris 10.